Human disease often involves changes in the timing and level of gene expression, processes investigated by transcriptomics, the identification of each expressed gene and its transcriptional levels. Studies of the association of human variation with altered gene expression can lead to a deeper, mechanistic understanding of disease states and can suggest therapies. A promising route to discovery is the transcriptomic analysis of novel models of common human diseases in aquatic species for which few genomic resources presently exist. Breakthroughs in sequencing technologies have opened the door for transcriptomics in non-model organisms. As detailed at the Sept. 2010 workshop 'Realizing the Scientific Potential of Transcriptomics in Aquatic Models', several impediments currently hinder the successful use of these tools in aquatic model systems. The goal of this project is to overcome these barriers by developing the protocols and tools necessary for researchers to capitalize on recent advances in DNA sequencing technology to better perform transcriptome analyses on aquatic medical models. This project will develop optimal laboratory protocols, analytical theory and computational software for transcriptome analyses of aquatic models of human disease and will help researchers plan and analyze experimental results. Protocols and tools will be made available via the Galaxy web platform as easy-to-use interfaces for computational software and web-based tutorials. Because many researchers working with aquatic non-model organisms lack access to the latest sequencing facilities and computational expertise for the analysis of high throughput transcriptomics, mechanisms will be developed for aquatic model organism researchers to use the Univ. of Oregon High Throughput Sequencing Facility. Similarly, many researchers lack access to computer clusters sufficiently powerful to execute the computational demands of modern transcriptomics, so this project will increase the availability of computational pipelines running at the Univ. of Oregon. This project will therefore provide widely needed tools, raise barriers to progress, and improve methods and technologies for transcriptome analysis in aquatic medical models, thus advancing our understanding of the role of gene regulation in health and disease.